data_2DA
# 
_chem_comp.id                                    2DA 
_chem_comp.name                                  "2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE" 
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H14 N5 O5 P" 
_chem_comp.mon_nstd_parent_comp_id               DA 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     1999-07-08 
_chem_comp.pdbx_modified_date                    2024-09-27 
_chem_comp.pdbx_ambiguous_flag                   N 
_chem_comp.pdbx_release_status                   REL 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        315.222 
_chem_comp.one_letter_code                       A 
_chem_comp.three_letter_code                     2DA 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        1QSY 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  EBI 
_chem_comp.pdbx_pcm                              Y 
# 
loop_
_chem_comp_atom.comp_id 
_chem_comp_atom.atom_id 
_chem_comp_atom.alt_atom_id 
_chem_comp_atom.type_symbol 
_chem_comp_atom.charge 
_chem_comp_atom.pdbx_align 
_chem_comp_atom.pdbx_aromatic_flag 
_chem_comp_atom.pdbx_leaving_atom_flag 
_chem_comp_atom.pdbx_stereo_config 
_chem_comp_atom.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_chem_comp_atom.model_Cartn_x 
_chem_comp_atom.model_Cartn_y 
_chem_comp_atom.model_Cartn_z 
_chem_comp_atom.pdbx_model_Cartn_x_ideal 
_chem_comp_atom.pdbx_model_Cartn_y_ideal 
_chem_comp_atom.pdbx_model_Cartn_z_ideal 
_chem_comp_atom.pdbx_component_atom_id 
_chem_comp_atom.pdbx_component_comp_id 
_chem_comp_atom.pdbx_ordinal 
2DA P      P    P 0 1 N N N N N N 0.327  28.898 -5.722  0.644  -0.205 -4.721 P      2DA 1  
2DA OP1    O1P  O 0 1 N N N N N N 0.447  27.871 -6.787  1.689  0.774  -4.350 OP1    2DA 2  
2DA OP2    O2P  O 0 1 N N N N N N 0.818  28.593 -4.355  1.327  -1.470 -5.446 OP2    2DA 3  
2DA OP3    O3P  O 0 1 N Y N N N N 1.077  30.250 -6.175  -0.407 0.485  -5.725 OP3    2DA 4  
2DA "O5'"  O5*  O 0 1 N N N N N N -1.210 29.310 -5.632  -0.124 -0.697 -3.395 "O5'"  2DA 5  
2DA "C5'"  C5*  C 0 1 N N N N N N -1.700 30.155 -4.602  -0.706 0.463  -2.800 "C5'"  2DA 6  
2DA "C4'"  C4*  C 0 1 N N S N N N -3.206 30.192 -4.637  -1.456 0.063  -1.527 "C4'"  2DA 7  
2DA "O4'"  O4*  O 0 1 N N N N N N -3.643 30.877 -5.839  -0.537 -0.425 -0.523 "O4'"  2DA 8  
2DA "C3'"  C3*  C 0 1 N N N N N N -3.893 28.839 -4.692  -2.099 1.304  -0.859 "C3'"  2DA 9  
2DA "C2'"  C2*  C 0 1 N N N N N N -5.232 29.191 -5.329  -2.221 0.852  0.616  "C2'"  2DA 10 
2DA "C1'"  C1*  C 0 1 N N R N N N -4.823 30.272 -6.330  -1.198 -0.292 0.746  "C1'"  2DA 11 
2DA N9     N9   N 0 1 Y N N N N N -4.537 29.758 -7.669  -0.218 0.030  1.785  N9     2DA 12 
2DA C8     C8   C 0 1 Y N N N N N -3.324 29.362 -8.182  0.956  0.698  1.607  C8     2DA 13 
2DA N7     N7   N 0 1 Y N N N N N -3.381 28.972 -9.432  1.580  0.811  2.743  N7     2DA 14 
2DA C5     C5   C 0 1 Y N N N N N -4.723 29.117 -9.765  0.845  0.230  3.721  C5     2DA 15 
2DA C6     C6   C 0 1 Y N N N N N -5.438 28.881 -10.959 1.013  0.041  5.104  C6     2DA 16 
2DA N6     N6   N 0 1 N N N N N N -4.879 28.428 -12.080 2.138  0.519  5.752  N6     2DA 17 
2DA N1     N1   N 0 1 Y N N N N N -6.766 29.130 -10.955 0.063  -0.602 5.775  N1     2DA 18 
2DA C2     C2   C 0 1 Y N N N N N -7.331 29.585 -9.824  -1.013 -1.061 5.164  C2     2DA 19 
2DA N3     N3   N 0 1 Y N N N N N -6.768 29.846 -8.646  -1.210 -0.913 3.871  N3     2DA 20 
2DA C4     C4   C 0 1 Y N N N N N -5.448 29.590 -8.685  -0.314 -0.283 3.118  C4     2DA 21 
2DA HOP2   2HOP H 0 0 N N N N N N 0.741  29.250 -3.673  1.776  -1.132 -6.233 HOP2   2DA 22 
2DA HOP3   3HOP H 0 0 N N N N N N 1.000  30.907 -5.493  -1.069 -0.185 -5.942 HOP3   2DA 23 
2DA "H5'"  1H5* H 0 1 N N N N N N -1.312 29.858 -3.599  -1.402 0.921  -3.502 "H5'"  2DA 24 
2DA "H5''" 2H5* H 0 0 N N N N N N -1.255 31.176 -4.653  0.079  1.176  -2.549 "H5''" 2DA 25 
2DA "H4'"  H4*  H 0 1 N N N N N N -3.485 30.695 -3.682  -2.213 -0.688 -1.750 "H4'"  2DA 26 
2DA "H3'1" 1H3* H 0 0 N N N N N N -3.318 28.037 -5.212  -3.080 1.511  -1.285 "H3'1" 2DA 27 
2DA "H3'2" 2H3* H 0 0 N N N N N N -3.960 28.302 -3.716  -1.447 2.174  -0.946 "H3'2" 2DA 28 
2DA "H2'"  1H2* H 0 1 N N N N N N -5.792 28.330 -5.762  -3.228 0.489  0.821  "H2'"  2DA 29 
2DA "H2''" 2H2* H 0 0 N N N N N N -6.035 29.485 -4.613  -1.965 1.671  1.288  "H2''" 2DA 30 
2DA "H1'"  H1*  H 0 1 N N N N N N -5.679 30.979 -6.426  -1.711 -1.221 0.996  "H1'"  2DA 31 
2DA H8     H8   H 0 1 N N N N N N -2.370 29.357 -7.628  1.316  1.078  0.662  H8     2DA 32 
2DA HN61   1HN6 H 0 0 N N N N N N -5.395 28.257 -12.942 2.240  0.386  6.708  HN61   2DA 33 
2DA HN62   2HN6 H 0 0 N N N N N N -4.392 27.562 -11.844 2.826  0.984  5.251  HN62   2DA 34 
2DA H2     H2   H 0 1 N N N N N N -8.417 29.771 -9.869  -1.760 -1.579 5.747  H2     2DA 35 
# 
loop_
_chem_comp_bond.comp_id 
_chem_comp_bond.atom_id_1 
_chem_comp_bond.atom_id_2 
_chem_comp_bond.value_order 
_chem_comp_bond.pdbx_aromatic_flag 
_chem_comp_bond.pdbx_stereo_config 
_chem_comp_bond.pdbx_ordinal 
2DA P     OP1    DOUB N N 1  
2DA P     OP2    SING N N 2  
2DA P     OP3    SING N N 3  
2DA P     "O5'"  SING N N 4  
2DA OP2   HOP2   SING N N 5  
2DA OP3   HOP3   SING N N 6  
2DA "O5'" "C5'"  SING N N 7  
2DA "C5'" "C4'"  SING N N 8  
2DA "C5'" "H5'"  SING N N 9  
2DA "C5'" "H5''" SING N N 10 
2DA "C4'" "O4'"  SING N N 11 
2DA "C4'" "C3'"  SING N N 12 
2DA "C4'" "H4'"  SING N N 13 
2DA "O4'" "C1'"  SING N N 14 
2DA "C3'" "C2'"  SING N N 15 
2DA "C3'" "H3'1" SING N N 16 
2DA "C3'" "H3'2" SING N N 17 
2DA "C2'" "C1'"  SING N N 18 
2DA "C2'" "H2'"  SING N N 19 
2DA "C2'" "H2''" SING N N 20 
2DA "C1'" N9     SING N N 21 
2DA "C1'" "H1'"  SING N N 22 
2DA N9    C8     SING Y N 23 
2DA N9    C4     SING Y N 24 
2DA C8    N7     DOUB Y N 25 
2DA C8    H8     SING N N 26 
2DA N7    C5     SING Y N 27 
2DA C5    C6     SING Y N 28 
2DA C5    C4     DOUB Y N 29 
2DA C6    N6     SING N N 30 
2DA C6    N1     DOUB Y N 31 
2DA N6    HN61   SING N N 32 
2DA N6    HN62   SING N N 33 
2DA N1    C2     SING Y N 34 
2DA C2    N3     DOUB Y N 35 
2DA C2    H2     SING N N 36 
2DA N3    C4     SING Y N 37 
# 
loop_
_pdbx_chem_comp_descriptor.comp_id 
_pdbx_chem_comp_descriptor.type 
_pdbx_chem_comp_descriptor.program 
_pdbx_chem_comp_descriptor.program_version 
_pdbx_chem_comp_descriptor.descriptor 
2DA SMILES           ACDLabs              10.04 "O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3"                                                                                                  
2DA SMILES_CANONICAL CACTVS               3.341 "Nc1ncnc2n(cnc12)[C@H]3CC[C@@H](CO[P](O)(O)=O)O3"                                                                                       
2DA SMILES           CACTVS               3.341 "Nc1ncnc2n(cnc12)[CH]3CC[CH](CO[P](O)(O)=O)O3"                                                                                          
2DA SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)[C@H]3CC[C@H](O3)COP(=O)(O)O)N"                                                                                      
2DA SMILES           "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)C3CCC(O3)COP(=O)(O)O)N"                                                                                              
2DA InChI            InChI                1.03  "InChI=1S/C10H14N5O5P/c11-9-8-10(13-4-12-9)15(5-14-8)7-2-1-6(20-7)3-19-21(16,17)18/h4-7H,1-3H2,(H2,11,12,13)(H2,16,17,18)/t6-,7+/m0/s1" 
2DA InChIKey         InChI                1.03  PUSXDQXVJDGIBK-NKWVEPMBSA-N                                                                                                             
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
2DA "SYSTEMATIC NAME" ACDLabs              10.04 "[(2S,5R)-5-(6-amino-9H-purin-9-yl)tetrahydrofuran-2-yl]methyl dihydrogen phosphate" 
2DA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2S,5R)-5-(6-aminopurin-9-yl)oxolan-2-yl]methyl dihydrogen phosphate"              
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
2DA "Create component"  1999-07-08 EBI  
2DA "Modify descriptor" 2011-06-04 RCSB 
2DA "Modify PCM"        2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            2DA 
_pdbx_chem_comp_pcm.modified_residue_id                TYR 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               P 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   OH 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
